I use NTFS on the Windows/program partition on my drive and FAT32 on the rest of the partitions. I went with this because of the increased securtity that NTFS offers (though I haven't done enough digging to find the security options), and because I heard it fragments less easially (wich IMO it does, but not by much).
The data is on FAT32 because when my last computer died, we ended up buying a program (which only reads FAT32) to recover the hard drive contents since the FAT died on us, and so I figure I might as well keep my data on a partition that I can recover from since I was so crazy without it when my pooter died.
JigPu